A Darker Time
by thewookieesroar
Summary: 19 Years after the Clone Wars end and Palpatines fall and all seems to be going well but there is a darkness that keeps nipping at the Jedi. It is a person but who could this sinister being be. Sequel to A Lighter Ending.
1. Chapter 1

**TIME SKIP: 19 YEARS INTO THE FUTURE.**

 **This is the first chapter of the time skip and I am going to make this a whole entirely new story so next chapter of this will be on a new story. But I might put this chapter in the new story too.**

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 **A Lighter Ending (continued)**

 **It is a dark time for the Jedi. Darkness is approaching. Not from the Sith but from something in the temple. Grand Master Yoda has sensed that it is a person that has darkness but is unable to figure out the puzzle. A Jedi Padawan was recently killed by this mysterious person.**

 **Supreme Chancellor Bail Organa has ordered Clone bases across the core to be on high alert. Furthermore, his term is coming to an end and the Jedi feel darkness in the next Supreme Chancellor election.**

 **Fearing for a new Clone Wars. The Jedi have begun to focus on their training but one question still remains. Is the threat from outside the temple, or from one of their own?**

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Anakin felt troubled. Tomorrow was the anniversary of the end of the Clone Wars and a big parade was planned but…. All he felt was darkness. Something tugged at him and told him that something bad was going to happen. He looked in the mirror and wondered if this was an omen for his death.

"Father. Let go, you have nothing to worry about." His daughter said from behind him.

Leia was nineteen now and Anakin could hardly believe it. She had also been recently appointed as the Jedi's representation in the senate. Not bad for a teenager.

"You don't understand the situation enough to make assumptions. I fear we cannot feel safe any longer." Anakin said.

"Yes father. I feel it but… I guess I don't feel it to the degree that you do." Leia said.

"You will feel it in time my young apprentice." Anakin said.

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Mace Windu and Yoda were out to lunch discussing the darkness. Yoda could feel it all around him and it seemed to haunt him like the Clone Wars.

"What should we do about this darkness?" Mace Windu asked.

"Already in motion, it is. Come to us it will, hmmmm." Yoda said.

"So we are still doing the parade right?" Mace Windu asked.

"Disappoint the citizens, we cannot. Suck it up for them, we will." Yoda said.

"So….." Mace Windu began.

"After lunch, talk about it we will. Changed my mind, I have. Want to enjoy lunch, I do." Yoda said.

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"So is everything all set? Is the plan still on?" Cad Bane asked.

"Yes. The Jedi Council will not see this coming. They feel too safe." The cloaked figure said.

"You want the same target. Is he still the one to die?" Cad Bane asked the figure.

"Yes. I have sent five thousand credits to you as a down payment and I have a ship waiting for you in the factory district. Once the target is dead I want you to run." The figure said.

"Got it boss." Cad bane said shutting off the comlink.

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Obi-Wan and his wife Ticarti were holding a party at their apartment. The kids, Luke, Leia, Shaak, Ticarti, and some kid named Ezra were gossiping about the happenings in the temple while the grownups were in more serious talks.

"I don't like this," Anakin began, "the dark side is too strong."

"I feel like Master Yoda is wrong. It might as well be an artifact of the dark side under our temple." Ticarti said as she watched her daughter talking to the other kids.

"Master Yoda can't be wrong." Padme said.

"He's Eight-Hundred and Ninety Six years old. He could be wrong. I do think we should trust Master Yoda though as he has been through more than anyone here at the temple." Ticarti said.

"I'm going to have my lightsaber ready at the parade." Anakin said.

"I agree." Obi-Wan said.

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As the parents had wrapped up their conversation. The kids were only taking off.

"And then suddenly a B2 Battle Droid came out of nowhere and I had to flip over it and slice it in half. I guess the Trade Federation still keeps those things active even though they aren't supposed too." Luke Skywalker said.

"Tell them about the Droideka!" Leia said. She loved this story because it was exciting but also because she was there.

"Leia and I were suddenly surrounded by those ancient droids. Suddenly our father came out of nowhere and threw these grenades that deactivated them. It was so cool. The final shutdown of the Trade Federation was my favorite mission!" Luke said.

"Definitely. The satisfaction of seeing Obi-Wan bring the slime ridden filth out to us in handcuffs was amazing!" Leia said.

"I can't even imagine what it was like fighting in the Clone Wars!" Luke said.

"I don't think you would survive another Clone War." Leia said making the others laugh at Luke.

"Well at least I'll die as a hero." Luke said smiling back at Leia.

"You should have been born to a smuggler." Leia said.

A voice out of nowhere interrupted them. "Alright everyone. It's time to go back to the temple. Parties over."

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 **This chapter wraps up A Lighter Ending but also starts A Darker Time. After A Darker Time ends than I will start a story I have been wanting to write for a while. Thanks for reading!**


	2. Chapter 2

**A Darker Time chapter 2! This is the parade but will also be when the darkness strikes. I'd like to thank you all for the reviews and ideas and would love for them to keep coming!**

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The council sat on their chairs on the float waving and smiling. With a guard of Clones how could they be touched?

"Master," Anakin started to say to Obi-Wan.

"I feel it also." Obi-Wan said sensing his friends concern. He didn't like it either but didn't want to disrupt the parade.

"I fear for everyone's life and cannot sense who the target is." Anakin said.

"Well my friend. Let's see where the force takes us." Obi-Wan.

"That's not the answer I was looking for." Anakin said.

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Cad Bane sat atop the roof waiting for the Jedi float to get close. He was instructed to only kill his target and he was fine with that because in this time, killing Jedi was a horrible idea but he needed the money.

"Alright scope. Safety off. Blaster charged." Cad Bane said to himself.

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Anakin and Obi-Wan both felt it but there was nothing they could do.

" **BANG"**

The looked around to see who got hit.

"MASTER YODA?!" Shaak Ti screamed.

There were screams in the crowd and Clones firing at the Bounty Hunter but they didn't care. Their beloved Master Yoda had just been assassinated.

"After that Bounty Hunter! Bring him to us alive!" Anakin shouted.

"We... Must… bring him back to… The temple." Obi-Wan said as he fought the tears.

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"Master Yoda was quite possibly the wisest Jedi of all time," Obi-Wan said in front of the whole temple at Yoda's funeral, "this funeral reminds me of my Master Qui-Gon's thirty-two years ago. We may never have another Master Yoda. The kindness and understanding that he had was legendary. He saw reason in everything. He was always curious about everyone and what more the force could give him. May the force be with you Master Yoda…. Always…"

Everyone got up and paid their respects to Master Yoda. Once everyone was done the council members went to the chamber to make decisions.

The eleven Jedi on the Council, Mace Windu, Anakin Skywalker, Obi-Wan Kenobi, Ahsoka Tano, Luminara Unduli, Shaak Ti, Aayla Secura, Depa Billaba, Saesee Tinn, Agen Kolar, and Stass Allie needed to elect a new Grandmaster and elect a new council member to the fill the empty slot.

"Let us start with appointing the new Council Member." Mace Windu said in his usual voice. As if he didn't even know that Master Yoda had died.

"I recommend Ticarti." Shaak Ti said as she wiped a tear from her face.

"That is a good suggestion." Mace Windu said.

"I don't know…" Obi-Wan said smiling making everyone smile a little.

"Than is it decided." Ahsoka asked.

"Yes. It is decided." Mace Windu said.

"Now we need to choose a Grandmaster. I believe Master Windu is a good option although Master Skywalker and Master Kenobi would also be good picks." Stass Allie said.

"Master Allie I would recommend you over myself." Obi-Wan said in disbelief.

"I don't want to have to deal with being Grandmaster." Stass Allie said.

"Than it is settled. I will be the new Grandmaster of the order." Mace Windu said.

"Master Windu we haven't even voted yet." Shaak Ti said.

"Who else is a better candidate than myself. I'm seventy-two years old and still one of the best swordsman in the temple and the wisest."

"Agreed." Saesee Tinn and Agen Kolar said in unison.

"But-." Shaak Ti began.

"Council dismissed!" Mace Windu yelled.

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Three figures with dark cloaks on sat in a room with a holonet in front of them.

"So you're sure you can win the upcoming election?" One figure asked.

"Yes I am positive." Said a Human Male with brown hair.

"Alright Admiral Motti. I am trusting you. I don't want to have gotten Master Yoda assassinated for nothing."

"I won't fail you Master Windu."

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 **Let this burn into your mind for a second…. What do you feel about this and who are the other two cloaked figures with Windu. Please leave a review!**


	3. Chapter 3

**What else is going to happen to the order in the next few days? Will Master Windu keep up his plans or will someone stop him? Who are the other two in the cloaks? We will find out.**

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Mace Windu was walking down the hallway. He watched as Padawans scurried out of his way. He walked into a room and locked the doors. In front of him were his two main allies. Saesee Tinn and Agen Kolar. They also saw the Jedi as weak and needing reform.

"I will need to eliminate my threats." Mace Windu said as he made sure the door was locked.

"I think Master Kenobi needs to be taken care of. He is a big threat, he almost beat you." Agen Kolar stated.

"We must quietly kill him. He is loved too much within the temple." Saesee Tinn said.

"I will deal with him myself. You two will back me up incase Skywalker comes to help." Mace Windu said.

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Anakin was walking through the hallways on this beautiful day. The light was shining through the temple windows. He saw people going towards where Master Yoda was buried. Master Yoda's death was a tragedy and something was off about Master Windu.

"Master Skywalker." Shaak Ti said greeting him.

"Hello Master Ti. Good to see you!" Anakin said.

"As to you Anakin. I would like to talk about the future of the order with you. I don't think Master Windu has great intentions." Shaak Ti said.

"Why not. He seems fine to me." Anakin said.

"Anakin something-." She was cut off as Anakin started running.

"I feel Obi-Wan is in danger! Follow me!" Anakin said.

Anakin arrived in the hallway and saw Master Windu dueling his Master except Master Windu was actually going for the kill. "Stop!" Anakin yelled.

Agen Kolar and Saesee Tinn came out of nowhere and ignited their lightsabers prompting Anakin and Shaak Ti to do the same.

"What are you doing?" Anakin yelled.

"What is best for the order!" Agen Kolar said.

A group of Padawans started watching the fight. "Padawans, go get help."

At this time Ahsoka had a group of temple security behind her. "Ahsoka! Help Master Kenobi!"

"Break it up!" A guard yelled as he got between Anakin and Agen Kolar.

"You should be ashamed of yourself Agen! You are turning to the dark side!" Anakin yelled.

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At lunch there were tons of guards around and nobody felt like fighting. At one table there was Anakin, Obi-Wan, Shaak Ti, Luminara, Ahsoka, and Aayla Secura who all believed that Master Windu was evil. At the other table was Mace Windu, Agen Kolar, Saesee Tinn, Depa Billaba and Stass Allie who believed Obi-Wan attacked Master Windu.

"I can't believe he would do that! That scum bag. I knew there was something wrong with him." Aayla Secura said.

Luke and Leia Skywalker came and sat next to their father and Master. "I was up in the security room when it happened and you can clearly see Master Windu ignite his lightsaber and try to kill Obi-Wan."

"If it wasn't for the fast reflexes I had to have training your father I would have died." Obi-Wan said chuckling a little.

"I'm going to talk to Chancellor Organa." Anakin said.

"We'll all come." Shaak Ti said forcing the others to stand up.

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Chancellor Organa was in his office reading a HoloMessage when the group of Jedi arrived. "Am I being arrested?" He asked smiling at them.

"No chancellor but this is a serious matter and we'd like to sit down with you and talk about it. We have Temple Guards outside the office not letting anybody in." Anakin said.

"Well sit down at the meeting table then." He said.

They all sat down and Chancellor Organa sat at the head of the table.

"What can I do for you." He said.

"We believe Master Windu is behind the assassination of Master Yoda and he hired Cad Bane. The day after almost a couple million credits came out of the Temple bank account and were given to a man we don't know and we suspect it was Cad Bane's fake bank account," Shaak Ti took a breath and continued, "Furthermore, we are planning on splitting the order. We feel it is no longer safe to be here so we are taking the loyal Padawans and Younglings to Tython and we would like a Republic fleet to escort us there."

"I will provide you a fleet but let me modify your plan. You will take a big portion of the Republic military with you including all your squads. From there they will train for the day you will retake the Jedi Temple. We must not let Master Windu get away with this." Bail Organa said.

"Then it is settled. Farewell Chancellor Organa. We hope to see you again." Anakin said.

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That night. The Jedi took all the babies and initiates from the temple onto a Republic cruiser and all the knights and Padawans that were loyal came aboard. Surprisingly, Depa Billaba's Padawan Caleb Dume joined them, although he changed his name to Kanan Jarrus so that he could conduct spy missions on Master Windu's faction.

"Next stop, Tython." Shaak Ti said as the five cruisers went into hyperspace.

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 **What do you think about this move? Also help me come up with names for Obi-Wan's faction and Mace Windu's faction. Reviews are much appreciated.**


	4. Chapter 4

**So sorry about the long wait. I have been caught up in school and haven't had much inspiration. Anyways, I am excited to write this chapter and need to write while my idea is still fresh.**

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Anakin was standing on the bridge of the cruiser thinking about the plan for Tython. Since the five weeks they had left, the Republic had sent them ten more cruisers with tons of Clones on them. The plan, blockade the planet and every ship coming to the planet is to be checked.

Tython was a planet that was dangerous to non-force users so the Clones would stay up in the cruisers to protect the planet. Down below, the Jedi had already rebuilt the old temple and driven away the Flesh Raiders.

Anakin heard a beep and answered a comm channel that was unknown. He looked at the figure and immediately recognized it was Riyo Chuchi.

"Riyo, what may I do for you?" Anakin asked wondering why the Pandoran Senator contacted him.

"Chancellor Organa has been overthrown and a Republic Military man loyal to Master Windu has taken control, that isn't what bothers me though, what bothers me is that Mace Windu killed him and said his final wish was for Mace to be chancellor. I'm afraid Mace Windu is the Supreme Chancellor of the Republic."

"Do you still control some parts of the fleet?" Anakin asked.

"The ones you control have been wiped from the database but the rest of the fleet is controlled by Windu. Luckily, the Clones are against Windu because I managed to hack into the database and turn them against Windu, the chip I have," she says showing him a chip, "has the information to turn them back onto Windu's side. I am coming out of hyperspace soon and need you to pick the chip up."

"Got it. We will await your arrival." Anakin said hanging up.

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Riyo Chuchi came out of hyperspace to see the biggest blockade since the Trade Federations Blockade of Naboo. She saw Tython, a forgotten planet whose only inhabitants were flesh raiders. She had never seen the Jedi, or the force's home world but she could immediately feel a burning light and she wasn't even force sensitive.

"Identification and business immediately." A voice of a Clone said over a comm channel.

"Senator Riyo Chuchi in need of a meeting with General Skywalker."

"Good to see you've arrived safely Riyo. Keep on your present course. Our tractor beam will bring you into the hangar." Came the voice of her friends husband Anakin Skywalker.

A few minutes later, she walked off the ship and was greeted by General Skywalker. A group of Clones went into her ship. She was confused. Anakin sensed he confusion and clarified.

"Although we know your friendly, you could have a stow away on board so we have Clones check your ship to make sure nothing funny happens." Anakin said.

"Makes sense. Here is your chip, I suggest you make it the highest guarded object on this planet." She said.

"We will." Anakin said tucking the chip away inside his utility pouch.

"Then I will be leaving." She said as she boarded her ship.

"Rex. Prepare a shuttle for me." Anakin said.

"Yes sir."

Anakin watched Riyo Chuchi's shuttle exit the cruiser and go into hyperspace. He had a bad feeling about what was to come but for now, he had to worry about this chip.

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The Jedi Order had changed since it moved to Tython. They had decided to call the New Jedi Order, the Tython Jedi Order, or Tython Jedi for short. The members of the council were:

Grand Master Obi-Wan Kenobi

Anakin Skywalker

Ahsoka Tano

Luminara Unduli

Shaak Ti

Aayla Secura

Luke Skywalker

Leia Skywalker

Stass Allie

Ticarti Mai

Furthermore, the studied and learned a lot. Kanan Jarrus had reported that the people who stayed were in the Senate all day and making sure Mace Windu could control the Republic. There were already uprisings on Naboo and Kamino. Spies inside the newly declared True Jedi Empire were sending new cruisers over all the time. Soon, they may have enough to occupy another planet.

That's what the council was meeting about. They were deciding on whether they should occupy a second planet and begin to fight back. All of their abilities had nearly doubled since Tython. Between conquering the lands of the Flesh Raiders and mapping out the planet, they had all seen a lot of action.

"I believe that if we do occupy a second planet it would possibly weaken our hold on Tython." Shaak Ti said as the meeting began.

"I think we should get along a big trade route or a big productive planet. Kessel or Corellia would be beneficial." Anakin said.

"I think we should check in with our spy on Coruscant." Obi-Wan said as he activated the Holotable entering the code.

"This is Jedi Knight Caleb Dume. Who am I speaking too?" He said. This phrase was the signal that nobody was around.

"Caleb. We are in a debate about the need to occupy a second planet. We would like to know what has been happening on Coruscant.

"Well Master Kenobi. I am hiding in the Underworld because Ex-Chancellor Organa led a legion of troopers over towards the Jedi Empire's Military Base. They all died and Organa has been taken hostage, the base suffered heavy causalities and most of the military is on Coruscant. Master Windu only cares about his safety. I'd say you could occupy Corellia no problem. Storming the capital may work, the Clones are uprising against Windu."

"I think it is time to take back what is ours. It's all or nothing. Caleb, last time you said you had a big army of people and Clones. Am I correct?" Obi-Wan asked.

"Yes."

"Do you have ships?" Obi-Wan asked.

"We have enough for a small fleet. No big cruisers."

"Well then, I guess we can bring the fleet. Prepare for the Second Battle of Coruscant."

"This will be the shortest lived Empire ever." Caleb said.

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 **Next chapter will be the Battle of Coruscant. Please leave a review and the reason they are taking this risk is because the fleet that is around the galaxy has no idea who their leader is so they are waiting fo Chancellor Organa or someone to contact them.**


	5. Chapter 5

**A Darker Time chapter 5. This chapter will be the Storming of Coruscant. There main ob**

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While in hyperspace, Anakin received a call from Riyo Chuchi. "Master Skywalker. I was gravely mistaken about the chip. It needs Master Windu's fingerprint to activate it. Furthermore, the Clones refuse to fight each other. I'm afraid that this will be a war between Jedi only."

"Alright. We are still going to storm the temple." Anakin said. The other Jedi around him nodded in agreement.

"Good luck. I will distract Windu with a conference." Riyo said.

"Thank you senator Chuchi." Anakin said.

The Jedi came out of hyperspace, they were immediately contacted by the Coruscant guard. "Identification and business."

"General Anakin Skywalker and Jedi business." Anakin said as he put his identification through.

Anakin hoped this wouldn't turn into a battle. They were severely outgunned.

"General Skywalker on the orders of the Galactic Senate we are not permitted to stop you. The Chancellor doesn't welcome you but we cannot stop you. Good luck in your Jedi business." The man said.

"Everyone get to the shuttles!" Anakin said to the whole fleet over the Holocomm.

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"What is the meaning of this meeting?" Mace asked.

"I want to discuss the future of the empire and how I can help." Riyo said.

"First, you can report anything you know about the Jedi traitors. Second, you can you can get Pantora and it's Militia to join the Empire. You can benefit from the empire, Pantora could thrive." Mace Windu said.

Lies.

Mace Windu had just lied to Riyo's face. She knew she couldn't count on Mace but she had to stall time for the Jedi.

"May I know how my world could benefit?" Riyo asked.

"I could make it a heaven for merchants. Think of the economy. Your planet could become a second Coruscant." Mace Windu said.

"I don't know if my people want foreigners on the planet." Riyo Chuchi said.

"I don't care what your pe-." Mace was cut of by his comlink beeping.

"Master, the Jedi Temple is under attack."

"Excuse me Senator." Mace said as he got up and started running.

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Obi-Wan engaged Agen Kolar. He almost cried as he was forced to kill a recently knighted Jedi. It was for the good of the order. These guys killed the greatest Jedi in a millennia and didn't even care. He kicked Agen Kolar and looked over at Anakin bravely dueling Master Billaba.

Agen Kolar jumped at Obi-Wan kicking him in the stomach. Obi-Wan fell back but recovered just in time to block Agen's next attack. He faked left and cut right fooling Agen and cutting him in half. He heard a speeder approaching.

"DIE TRAITORS!" Yelled Mace Windu.

Shaak Ti went to confront Mace Windu only to get hacked down and killed. Next was Luminara who blocked one strike but succumbed to the second strike.

"Stand back." Anakin yelled as he and Obi-Wan stepped forward.

"You. Will. Die." Mace said charging them. The rest of the Jedi held off the remnants of Mace's order.

Anakin jumped at Mace and struck towards his head. Mace blocked with almost no effort and pushed Anakin into a building knocking him out. He threw his saber at Anakin but it was blocked by Luke Skywalker. Luke jumped at Mace and swiftly brought his saber down countering Mace's moves. Obi-Wan brought his blade back but he was pushed a little and would have been pushed farther if Luke didn't interrupt Mace's force push.

"Can't beat Master Kenobi that easily." Luke said smiling at the corrupted Master.

Mace brought his Lightsaber down on the boy and knocked the lightsaber out of his hand. He was just about to strike the killing blow when Obi-Wan force pushed the boy away catching Windu off guard. Windu was pissed. He almost killed a Skywalker.

"YOU ARE DEAD!" He screamed.

He hacked at Obi-Wan blow after blow until the old man couldn't hold any longer. Suddenly, the blows stopped. He looked up to see Luke overpowering Windu. Blow after blow was dealt to Windu, it was as if the boy was being controlled by Revan or Yoda. Luke hit Windu's lightsaber out of the way and then stabbed him through the stomach.

It was over.

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Luke looked down at his fallen opponent. He had just beaten the man that had killed two great Masters and Clone war veterans. All at the age of eighteen. All he had done was trust in what the force told him to do.

He looked back at his peers. His father had waken up and was walking towards him along with Obi-Wan. They smiled at him and walked over to wear the bodies of Shaak Ti and Luminara lie.

"They were great Jedi." Anakin said as he picked up the body of Shaak Ti and started bringing her to the temple.

"Now all we have to do is rebuild." Obi-Wan said as he picked up Luminara's body.

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 **Well that was the final chapter. I know this was a short story but I have better projects coming. I will write on last chapter if you want but it will be of the rebuild but if you guys want it I will most certainly write it.**


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